XDOM, a graphical tool to analyse domain arrangements in any set of protein sequences.
BACKGROUND
To extract the maximum possible information from a set of protein sequences, its modular organization must be known and clearly displayed. This is important both for structural and functional analysis.


RESULTS
This paper presents an algorithm and a graphical interface called XDOM which performs a systematic analysis of the modular organization of any set of protein sequences. The algorithm is an automatic method to identify putative domains from sequence comparisons. The graphical tool displays the proteins as a set of linked boxes, corresponding to its domains. The method has been tested on a family of bacterial proteins and on whole genomes. It is currently applied to the complete SWISS-PROT database to build the PRODOM database.


BACKGROUND
XDOM is available free of charge by anonymous ftp:¿¿ftp://ftp.toulouse.inra.fr/pub/xdom¿ ¿. The ProDom database can be consulted at ¿¿http://protein.toulouse.inra.fr/prodom.html¿¿.
Gouzy
J
J
Laboratoire de Biologie Moléculaire des Relations Plantes-Microorganismes, INRA/CNRS, Castanet-Tolosan, France. [mailto:fcorpet@toulouse.inra.fr]
Eugéne
P
P
Greene
E A
EA
Kahn
D
D
Corpet
F
F
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D003198:Computer Simulation; D016208:Databases, Factual; D016680:Genome, Bacterial; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D012985:Software Design